Comment

Note that default value for InnoDB logs has changed in 5.6 from 5MB in previous versions to 48MB. InnoDB will refuse to start if it encounters existing logs size different then default or specified value. So you can just copy responsible setting from 5.5 instance (innodb_log_file_size = 5242880), or just move those files out of datadir and start MySQL. InnoDB will re-create new logs.
However for most production cases, much larger logs are advised, like 1GB+.

Comment

As przemek mentioned, the easiest way to solve the innodb_log_file_size issue would be move the ib_logfile* files from the MySQL 5.6 data directory to another location for safe keeping, then start up the MySQL 5.6 instance. That will force MySQL to create new ib_logfile's with the new size. Keep in mind that you will have to do that anytime you do a binary restore (i.e. with Xtrabackup) from another MySQL server with a different innodb_log_file_size.

Note that the ib_logfile files are important, so under normal circumstances you would not want to mess with them unless you know what you are doing, but it should be safe in this case.